Seed Magazine: Apuntes Para El Siglo Xxi

  • December 2019
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The Key Question in Climate Science:

Seed’s Tear-outable tool for living in the 21st century Cribsheet #2

How much will the earth’s temperature rise as humans double the amount of carbon dioxide in the atmosphere through use of fossil fuels?

CLImAtE chAnge The Greenhouse effect 1

7

SOLar radiation

Radiation from the sun enters the atmosphere. Some of it is reflected back into space, but a good portion is absorbed by the atmosphere and the earth’s surface. 2

Infrared radiation

The surface, in turn, heats up and emits infrared radiation. 3

clouds As the earth warms, more water evaporates, creating more clouds. Since clouds are white and reflective, they bounce a lot of sunlight into space, which would have warmed the earth. This is negative feedback. At the same time, clouds are made up of concentrated greenhouse gas, and can also provide positive feedback. Clouds will play an important role in climate change, but no one is sure yet whether they will ultimately end up warming or cooling the earth.

Greenhouse gas

Greenhouse gas molecules absorb radiaton from the sun and earth, heat up, and emit infrared radiation. Some infrared radiation is directed back toward the earth, contributing to the warming of the surface.

6

Feedback 4

What are FEEDBACK LOOPS?

Feedback loops are self-perpetuating cycles that enhance or dampen the greenhouse effect. The ones illustrated here are just a few examples of the many feedback loops at work on the climate. Without feedback, humans could double the amount of CO2 in the atmosphere (which we’re in the process of doing) and the earth’s average temperature would rise by about 1.2ºC. That’s enough to cause noticeable changes in climate, but probably not catastrophic ones. With feedback the problem is more complicated. It boils down to climate sensitivity: Will negative and positive feedbacks cancel each other out, or will they cause a catastrophic rise in temperature?

5

Water vapor

Water vapor is a greenhouse gas, and helps to warm the earth. At higher temperatures, more water evaporates, putting more water vapor into the air, which heats the earth even more. This is another important positive feedback loop.

Global Temperature and co2

CLIMATE treaty map 380

.8

Each point on the temperature line represents an average taken over five years. The global temperature average taken for 1935-1940, for instance, is just under 0.1ºC above the baseline.

.6 .4 ˚C

360 340

.2 0

Sea ice

Ice is reflective. When sunlight is reflected into space, it doesn’t contribute to the greenhouse effect. So the ice caps help to limit warming. As things heat up, the ice melts, revealing the darker ocean beneath, which absorbs more radiation and warms, melting more sea ice. This cycle is a positve feedback loop.

ppm Global temperature average (1950–1980)

320

-.2

300

-.4

ILLUSTRATION: SILO

Year

-.6

280 1900

The issue:

1920

1940

1960

1980

2000

Global Temperature Change (5-year mean)

Kyoto Treaty Members

Members of both

Atmospheric CO2 Concentrations

Asia-Pacific Partnership for Clean Development and Climate Members

No action

What is the best way to deal with these changes?

The earth’s average temperature is likely to rise by 2º to 6º C as a result of a projected doubling of the amount of CO2 in the atmosphere from preindustrial levels, to 560 parts per million by mid-century. The effects could be severe. Sea levels could rise by as much as 6 meters as the icecaps melt; deserts may become larger, storms more severe, heat waves more common, and snow could turn to rain, reducing our ability to collect water for drinking and irrigation. The Kyoto Protocol, effective this year, is an agreement by member nations to limit their carbon emissions. The alternative supported by the U.S. and Australia, the Asia-Pacific Partnership, seeks to incentivize the creation and deployment of green technologies, but doesn't limit carbon emissions and sets no target dates.

soundbite More carbon dioxide was added to the atmosphere in the past 200 years than between the last Ice Age and the Industrial Revolution.

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The Key Question in nuclear engineering:

Seed’s Tear-outable tool for living in the 21st century Cribsheet #5

How can reactors be designed to work at maximum efficiency, to be safe and self-regulating, and to minimize nuclear waste?

Graph Data: IAEA

Nuclear Fission

2

Nuclear fission occurs when a neutron strikes the nucleus of an atom and splits it apart. Most of the nucleus of the original atom goes to form new, smaller atoms. In addition, several neutrons may split off from the original atom during fission. But the mass of all these neutrons and fission products does not add up to the mass of the original atom. That’s because when the atom splits, some of its mass is converted directly into energy.

steam generation

This superheated water is pumped through a pipe that runs, like a heating element, through a second chamber called the steam generator. The steam generator is partially filled with clean water, which is boiled by the heated pipe running from the reactor generator vessel. The steam generator is also kept at high pressure (though it’s lower than that of the reactor vessel).

steam generator

turbine 2 3

Illustrator: Cybu Richli - www.cybu.ch

3

Nuclear reactors and warheads can employ the uranium isotope U-235. When the U-235 atom splits, it frees two or three neutrons, which then fly off and split other U-235 atoms in close proximity, starting a chain reaction.

4

pump

condenser

control rods

cooling tower

BASIC PRINCIPLE Heat flows from one part of the power plant to the next. As one part warms up, heat flows out of the previous one, allowing it to cool, so safe operating temperatures are maintained.

In warheads, the chain reaction multiplies exponentially, giving off a huge amount of energy at once in a nuclear explosion. In nuclear reactors, a chain reaction must be controlled to create a safe, harvestable source of energy.

1

4

the nuclear reaction

In the reactor vessel, cylindrical uranium pellets are stacked into long fuel rods. It is within bundles of these rods that the chain reaction occurs. Together they are called the reactor. To keep the reaction under control: • Low concentrations of U-235 are used in the reactor, so not every neutron will strike a nucleus. • Retractable control rods, made of a material that absorbs neutrons, can be lowered into the reactor to siphon off neutrons that would otherwise multiply the chain reaction.

Much of the energy released by the chain reaction is manifested as heat. The fuel rods are placed inside a pressurized chamber full of water. Because this reactor vessel is kept at high pressure, the water will reach temperatures much greater than 100º C.

world energy consumption by source Nuclear Hydro Biomass Gases Solids Liquids

350 300 250 200

100 50

1018 JOULES

150

0 1970

Superheated steam forces its way out of the steam generator. It cranks a turbine, which produces electricity. As the water in the steam generator boils, it also siphons heat away from the water in the pipe flowing to the reactor vessel. This helps to cool the reactor. In another type of nuclear plant, called a boiling water reactor, the steam powering the turbine comes directly from the reactor vessel.

steam condensation

reactor vessel

self regulation Modern reactors are designed to be safe and self-regulating. In the same way that an airplane is designed to level out naturally after being jostled, reactors are engineered to maintain safe levels of chain reaction under any circumstances.

power needs supplied by nuclear plants

450 400

electricity generation

After the steam cranks the turbine, it is condensed back into a liquid as it runs over a pipe filled with cold water flowing from the cooling tower. It is then recycled into the steam generator. The water from the cooling tower heats up during this process and some of it is released as steam. It is then replaced from a nearby body of water.

reactor

6.34% 2.22% 6.75%

This graph shows the steady increase in global energy consumption since 1970. Combustible liquid and solid fuels, like gasoline and coal, remain our dominant sources of energy.

23.04%

26.08%

(EQUIVALENT TO 23.9 MEGATONNES OF OIL)

Writer: Joshua Braun

Consultants: Per Peterson and Daniel Kammen, Professors, Nuclear Engeneering at UC Berkeley

Map Data: The Nuclear Energy Institute / The International Atomic Energy Agency (IAEA)

1

Percent by country 35.09% Year

1975

1980

1985

1990

1995

2000

1-20 20-40 40-60 60-80

2004

The issue: Why are some people concerned about nuclear power?

soundbite

Uranium used in reactors has been enriched to create a higher concentration of U-235 than occurs in nature. Countries with the technology to enrich uranium for power can expand their capabilities to create highly enriched uranium for weapons. Some reactors use plutonium, another weapons material, or create it as a waste product. Due to proliferation concerns, the International Atomic Energy Agency keeps close tabs on how and where nuclear materials are used. Even regular nuclear waste—the radioactive and heavy metals that are the products of fission—is dangerous, making it a concern everywhere nuclear power is used.

Nuclear reactors are an important carbon-free source of power. We are likely to see a surge in their construction in the next few years.

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ILLUSTRATION NOTE The sample biome includes a river, an ocean, a volcano, and a glacier. Geometric shapes such as spheres, cones, and icosahedrons indicate different species, and deceased organisms are darkened.

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light CriBsheet #13

What is light and where does it come from? How can light be used to investigate the world around us?

Light is energy that travels as a wave through space. Most of the light we encounter in everyday life is produced by nuclear fusion in stars or the energetic excitation of electrons in atoms. A wave of light actually has two components: an electric field, and a magnetic field. Consequently light is also called electromagnetic radiation. Electricity and magnetism are interdependent: One can produce the other. Similar to how passing a magnet over a coil of copper wire briefly generates electricity, or how a constant electric current can magnetize iron, a light wave‘s oscillating electric and magnetic fields reinforce each other and propagate through empty space at nearly 300,000 kilometers per second. This value is known as the speed of light, and appears to be the universe‘s ultimate speed limit—nothing travels through space faster.

Magnetic field

Electric field

Wavelength 1 2

Lower energy / Longer wavelength

Higher energy / Shorter wavelength

All forms of light—radio waves, microwaves, infrared, visible, ultraviolet, x-rays, and gamma rays— are identical except for their wavelength. Light‘s wavelength determines its energy; the shorter wavelengths have higher energy. Light from most natural sources contains multiple wavelengths. White light contains all visible wavelengths. Refracting it through a prism separates them into a continuous spectrum .

Interference pattern

3

LIGHT aND MaTTER Ejected electron Low intensity, high energy light

Metal plate

High intensity, low energy light Light source

WaVE-PaRTICLE DUaLITY

Light usually behaves like a continuous wave, but it can also act as if it is composed of discrete particles of energy called photons. Light‘s wave-like nature can be revealed when light diffracts through two slits and shines onto another surface. Light passing through the slits acts as two waves that disrupt and interfere with each other. Where the waves‘ peaks and troughs overlap, they combine to produce a characteristic interference pattern of light and dark bands.

But when light of different wavelengths shines on a metal surface, the existence of individual photons becomes clear. If an electron in the metal absorbs more than a threshold amount of energy, it breaks free and zips away. Since shorter wavelengths contain more energy, a very bright but long-wavelength light will have no effect on the metal, while a very dim but short-wavelength light will release electrons. The energy of ejected electrons increases not with greater amounts of light, but with more energetic wavelengths. This means each electron ejection depends on the energy of an individual photon.

The Electromagnetic Spectrum

Writer: Lee Billings Illustrator: Cybu Richli — www.cybu.ch

Microwaves

Infrared

Ultraviolet

Because light can originate from the excitation of electrons in atoms, and each element of the periodic table has a unique atomic configuration of electrons, the elemental composition of any substance can be discovered through observing the spectrum it produces when its electrons are energized. For instance, burning a sample of hydrogen gas creates light. Running that light through a prism produces a distinct emission spectrum 2 . Conversely, light passing through a cool cloud of hydrogen gas and then a prism produces a unique absorption spectrum 3 . By studying spectra like these, we can measure the chemical composition of practically anything on Earth, as well as the atmospheres of other planets, the Sun, and even the distant stars.

Redshift/ Blueshift X-rays

Gamma rays

Visible

Reference: Universe, Robert Dinwiddie et al., DK Publishing Inc., 2005

Radio waves

Each kind of atom in a substance absorbs characteristic wavelengths of light; all other wavelengths are reflected back or transmitted through. Different mixtures of atoms reflect different wavelengths, creating the diversity of colors we perceive in the world around us.

Wavelength 10km 1km

100m 10m

1m

10cm

1cm

1mm

100µm 10µm 1µm

100nm 10nm 1nm

100pm 10pm 1pm

100fm 10fm 1fm

In theory, light‘s shortest possible wavelength is trillions of times smaller than the diameter of a proton, and light may have no upper limit on its wavelength. In practice, we can detect light with wavelengths ranging from thousands of kilometers down to less than the size of an atomic nucleus. The electromagnetic spectrum is the continuum of wavelengths between these extremes. Our eyes can only see light between 400 and 700 nanometers in wavelength— a miniscule portion of the entire electromagnetic spectrum.

THE ISSUE: Harnessing Light

Like the sound of a passing siren that rises and then falls in pitch as it approaches and recedes, light waves from a source moving in relation to an observer exhibit similar shifts. As a light source approaches an observer its light is compressed to shorter wavelengths — this is a blueshift. As a light source recedes, its light is stretched— this is a redshift. The redshifts and blueshifts for most slow-moving, earthbound objects are too small to be easily noticed. But on astronomical scales, we can measure the motions of planets, stars, and galaxies using this effect.

Many of the past century‘s major scientific and technological advances came from studying the physics of light, and this trend is certain to extend well into the future. Our understanding of light has allowed us to study the universe on the smallest and largest of scales. It has given us applications like radio, television, radar, medical x-rays, microwave ovens, and wireless computer networking, to name but a few. Now, emerging technologies like quantum computing, efficient solar power, and light-based spacecraft propulsion are poised to further transform science and our society.

SOUNDBITE Light is electromagnetic radiation that moves through space at 300,000 kilometers per second and acts as both a wave and a particle.

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exoplanets In 1543, Polish astronomer Nicolaus Copernicus published On the Revolutions of the Heavenly Spheres, showing that the Earth, far from being the privileged center of the universe, is just another planet orbiting the Sun. Since then, the discovery that our Sun is a typical star among the billions in the Milky Way, which in turn is but one of the billions of galaxies we observe in all directions, has strengthened the notion that our place in the universe is merely ordinary. This assumption of our cosmic mediocrity is called the Copernican principle.

Do planets form around other stars? How can we detect and study them? Are there other planets like Earth?

But perhaps the Copernican principle is wrong. Compared to other terrestrial planets in our solar system, the Earth seems special. It alone has oceans of water, plate tectonics, and a large moon. As far as we know, it alone hosts life. Since the first detections of planets orbiting other stars in the mid-1990s, we've discovered hundreds of exoplanets, but none resembles the Earth. Could we and our world be unique? In the near future, this question will be answered by one of three detection methods: stellar radial velocity, planetary transits, and gravitational microlensing.

microlensing

Gravitational microlensing is a newer technique to find exoplanets that uses effects predicted by Einstein's theory of general relativity. Just as a magnifying glass can enlarge an image, a star's gravitational field can bend space and magnify light in a process called microlensing. When a distant bright star aligns with a dimmer lensing star that is closer to Earth, the distant star’s light brightens A . If planets orbiting the lensing star are perfectly aligned, they too will magnify the distant star's light, allowing astronomers to estimate their mass and orbital distance B . Microlensing works best for planets orbiting their stars at Earth-Sun distances or greater. Since each chance alignment only occurs once, microlensing can't be used to closely study individual planetary systems, but rather provides a statistical sample of exoplanet populations.

radial velocity

A planet orbiting a star causes the star to “wobble” back and forth. The radial velocity method detects this wobble by examining the color of starlight: As the star moves toward an observer, its light becomes bluer ; as it moves away, its light becomes redder 2 . By analyzing these color shifts over time, the presence of planets, along with their masses and orbits, can be inferred. So far most exoplanets have been found using radial velocity measurements.

Absorption Spectrum 2

1

Brightness

Time

3

Time

Lightcurve

A

B

Brightness

Lightcurve

Background Star

planetary transits

Lensed Image

The transit method finds planets by looking at the total amount of light from a star over time. If a planet passes in front of its star as viewed from Earth, the star's light slightly dims during the planet's transit 3 . Measuring how much the starlight diminishes reveals the planet’s diameter. Many exoplanets can be studied with both radial velocity and transits. The combined data can allow astronomers to estimate not only a planet's size, mass, and orbit, but also its density, temperature, and atmospheric composition.

Planet Lensing Star Telescope

Both radial velocity and transit methods overwhelmingly favor detecting Jupiter-mass planets that orbit their stars at a fraction of the distance between Mercury and our Sun. 1

refining the search

2

3

4

haBitaBle zones

1 HD 16141 b

Habitable Zone

2 0.1

51 Peg b

Mass of star relative to Sun

Planetary Mass (1= Jupiter)

Illustrator: Southsouthwest — www.southsouthwest.com.au Writer: Lee Billings Consultant: Greg Laughlin, Professor of Astronomy and Astrophysics, University of California, Santa Cruz. Habitable Zone: Derived from an image created by Gabriel Rodriguez Alberich, viewable at http://en.wikipedia.org/wiki/Image:Habitable_zone-en.svg. This Habitable Zone image is used and released under the terms of the GFDL (http://en.wikipedia.org/wiki/GNU_Free_Documentation_License). Lowest Exoplanet Masses: Jean Schneider's Extrasolar Planets Encyclopedia, http://exoplanet.eu/

CriBsheet #14

55 Cnc e

HD 75289 b Gl 581 c HD 49674 b Earth

0.01

0.001 1995

OGLE-05-390L b

Jupiter

Mercury 0

2005

2010

2015

The vast majority of detected exoplanets have been gas giants like Jupiter and Saturn that closely orbit their stars. But as observational data accumulate and new search projects come online, scientists have begun discerning the telltale signatures of smaller, terrestrial exoplanets several times the Earth's mass. This graph plots the diminishing size of the smallest known exoplanets: In little more than a decade, the record has dropped over an order of magnitude. Extrapolating from this trend, astronomers should begin detecting Earth-mass exoplanets around 2011 or 2012, though this may happen much sooner.

THE ISSUE: discovering haBitaBle worlds

Uranus

Neptune

1

0.5 2000

Saturn

0.1

1

Venus 10

Not to scale

Earth

Mars

40 Radius of orbit relative to Earth’s

Life as we know it requires liquid water. If a planet orbits its star too closely, any water evaporates into steam; too far away, and water freezes into ice. The sweet spot between these extremes is the "habitable zone" (HZ). A star's mass determines its HZ; the more massive a star is, the brighter it shines, pushing the HZ further out. Astronomers now believe the first Earth-mass exoplanet within an HZ will be found around a red dwarf, the smallest, dimmest, most numerous type of star in our galaxy: Planets in a red dwarf's HZ orbit so closely that they should be detectable with radial velocity or transit searches.

Astronomers using radial velocity, transit, or microlensing searches are racing to discover the first Earthlike exoplanet. New telescopes, improved data analysis, and the realization that red dwarf stars are excellent planet-hunting targets imply that the first Earth-mass exoplanet in a “habitable zone” will be found in the next few years. If that planet transits its star, we may be able to analyze its atmosphere. If its atmosphere contains water, oxygen, carbon dioxide, and methane, we’ll have found more than a habitable world—we’ll have discovered the first credible signature of alien life.

SOUNDBITE We have found nearly 300 exoplanets using radial velocity, transits, and microlensing, and are likely to find an Earth-mass exoplanet in the near future.

Seed’s Tear-outable tool for living in the 21st century

the Key Questions of Quantum computing:

CriBsheet #15

What is a quantum computer, and how does it differ from modern computers? How can we use quantum computing?

QUANTUM COMPUTING Intel cofounder Gordon Moore famously observed nearly half a century ago that the number of transistors economically crammed into a single computer chip was doubling every two years. This trend toward miniaturization is seen throughout the history of modern computing. Today elements of microchips are only tens of nanometers in size, and if miniaturization continues, microchip components will eventually reach atomic scales, where their properties will be dictated by quantum mechanics.

Hundreds or thousands of qubits would be needed to factor very large numbers. For convenience, here we’ve illustrated only four.

The encryption vital for modern secure communications assumes that factoring large numbers in a reasonable amount of time is beyond the capabilities of today’s commercial computers. In 1994 computer scientist Peter Shor devised an algorithm allowing a quantum computer to quickly factor large numbers. Thus, a powerful quantum computer could break the world’s dominant encryption schemes, resulting in the need for new security methods. For perspective, today’s quantum computers are scarcely powerful enough to factor a number like 15. At right, a schematic illustration outlining how Shor’s algorithm works:

Place the qubits in a superposition over all of their possible configurations in preparation for initiating a quantum interference pattern.

interference patterns The latent possibilities within a superposition can actually interfere with each other, constructively reinforcing or destructively canceling each other to form the final definite state. The programmer of a quantum computer must choreograph the calculation in such a way that computational paths leading to a “wrong” answer will destructively interfere with each other, canceling each other out and leaving only the “right” answers to be observed.

Choreograph quantum interference to allow paths to correct answers to reinforce each other.

quantum computing 101 0

FINDING aN aNSWER

The ability of quantum objects to simultaneously hold multiple, seemingly conflicting values is at the heart of quantum computing. This state is called a quantum superposition (at right). Superpositions occur all the time at the quantum level. In fact, any isolated quantum object like an atom or a photon is in a superposition. But as soon as the object interacts with something else, such as another atom or photon, the superposition is liable to collapse. The collapse of a superposition is called decoherence. Decoherence is essentially an act of measurement, where all possible states in the superposition collapse into the one ultimately observed. If the quantum computer’s qubits suffer too much decoherence before the calculation is completed, the information will be irretrievably lost and the probability of producing a correct answer becomes essentially zero.

1 Both classical and quantum computers perform calculations by manipulating information. Classical computers represent information as binary digits, or bits, which can have values of either 0 or 1. Quantum computers represent information as quantum bits, or qubits. Many different physical objects can be used as qubits, such as atoms, photons, or electrons. Paradoxically, a qubit can represent 0 and 1, as well as other possible values, at the same time, in what is called a quantum superposition. This allows a qubit to simultaneously use many more informational states for computation and is responsible for quantum computing’s advantages over classical computing. In the illustration above, an atomic spin represents a qubit. An “up” spin corresponds to 0; a “down”spin equates to 1. A quantum superposition encompasses 0, 1 and all possible values in between.

Perform a measurement, collapsing the qubits’ superposition. By repeating these steps and combining the results, we can reliably obtain the factors of a very large number.

What ProBlems Can a Quantum Computer Solve?

NP

Easily solved by quantum computers

BQP

Easily solved by classical computers

P

Factoring a very large number Testing if a number is prime

Computer scientists classify a problem’s difficulty by the number of computational steps an algorithm requires to solve it. Problems that a classical computer can quickly solve are called P (polynomial time) problems. In P problems, as the problem size n increases, the number of steps to solve it grows polynomially, for instance by n2. Determining whether a number is prime is an example of a P problem. NP (nondeterministic polynomial time) problems consist of all problems for which the answers are easy to check, even though finding those answers may take an exponential number of computational steps,

Computational time

Illustrator: Thomas Porostocky — www.porostocky.com Writer: Lee Billings Consultant: Scott Aaronson, Assistant Professor of Electrical Engineering and Computer Science, Massachusetts Institute of Technology

Miniaturization may ultimately lead to quantum computers, which use quantum effects to perform calculations. Quantum computers could, in principle, solve certain problems exponentially faster than the best known “classical” methods with far-reaching consequences for cryptography and the simulation of quantum physics. Simple quantum computers have already been built, but most experts believe robust and powerful systems remain many years away.

2n n2 n 0

1

2

3

4 5 Problem size (bits)

6

7

8

9

such as 2n. Every P problem is also an NP problem, but computer scientists believe that not all NP problems are P problems. BQP (bounded-error, quantum polynomial time) problems are the class of problems that quantum computers can efficiently solve. Factoring the product of two large prime numbers is an example of a problem that is both an NP and a BQP problem. Though no one knows for certain, it appears that BQP does not include most NP problems. This means that for most NP problems, quantum computers may offer no significant advantages over classical computers.

THE ISSUE: can we Build a sophisticated quantum computer?

A company called D-Wave Systems has exhibited what it controversially calls the world’s first commercial quantum computer, but most experts treat these claims with considerable skepticism. Some of the best minds in physics today are struggling to build simple quantum computers, and computer scientists are still seeking their ideal applications. It seems that even if practical, powerful quantum computing existed today, we probably wouldn’t know how to best use it. Ironically, if building sophisticated quantum computers turns out to be impossible in principle, this may be the biggest breakthrough of all, as it would imply that our fundamental understanding of the quantum world is incorrect.

Quantum computers could theoretically revolutionize our ability to solve certain kinds of computational problems, but first we must discover how best to build and use them.

Seed’s Tear-outable tool for living in the 21st century

the Key Question of SYNTHETIC BIOLOGY:

CriBsheet #16

SynThetic biology

Can we learn to program DNA and living organisms as well as or better than we currently program computers?

Life, even at its most minuscule, can elicit incredible change on a planetary scale. Consider the oxygen you’re breathing. Its presence in Earth’s atmosphere is a biochemical accident, a waste product of photosynthesizing organisms. Together, organisms cycle essential nutrients like carbon and nitrogen around the planet; even on its own, an organism can fabricate useful materials, and each—thanks to its cellular machinery—is capable of processing the information found in its genetic code.

Biotechnology Basics

1

constructing dna DNA sequencing allows researchers to read genetic material, converting information encoded within DNA molecules into sequence data. DNA synthesis allows biologists to write genetic material from scratch, using sequence data to assemble DNA molecules 1. Researchers are working to improve the power of DNA synthesis technology, but the bigger challenge is to invent new languages and grammars that enable the writing of many new genetic “programs,” each coding for useful behaviors, such as the production of fuels, foods, or medicines.

After biologists learned to decode genes, they soon learned to redirect the power of life by manipulating DNA. Scientists have developed numerous techniques to read and modify DNA; those techniques form the basis of genetic engineering, but many are inefficient. Synthetic biology is an effort to develop better tools and technologies for engineering biological systems, with the overarching goal of creating new biological functions and enhancing those that already exist.

Sequence data

Genetic information is encoded by four nucleotides, or bases, that are part of DNA’s molecular structure. To obtain this information, scientists read these bases in a process called DNA sequencing 1. Once a sequence is known, it can be isolated by restriction enzymes, proteins that sever DNA strands at specific sequences 2. A genetic engineer can insert such snippets of DNA into other DNA strands 3. Snippets of DNA can also be amplified (copied many times) by the polymerase chain reaction (PCR), making them easier to work with 4. Polymerases are molecules that travel along a strand of DNA to perform various tasks. Researchers also use PCR to selectively mutate small portions of genes. These methods enable researchers to manually edit DNA, which can then be incorporated into living organisms via several techniques collectively called DNA transformation.

...GATTACAGATTA... Raw materials (bases)

Synthetic DNA

2 RNA polymerase Extracellular signaling molecule

Illustrator: Thomas Porostocky — www.porostocky.com Writers: Lee Billings and Drew Endy Consultant: Drew Endy, Assistant Professor of Biological Engineering, Massachusetts Institute of Technology

genetic programs To make programming DNA easier, synthetic biologists are creating banks of standardized DNA sequences, or parts, that each perform a specific function. For example, the BioBricks Foundation, an open-source initiative from MIT, Harvard, and the University of California, San Francisco, is doing this by developing BioBrick parts, functional sequences of DNA with uniform prefix and suffix sequences. This structural standard allows BioBrick sequences to link together and act as interchangeable parts.

1 BioBrick receiver

3

4

2

=

+

3

An efficient genetic machine also requires a communications standard. For example, one type of BioBrick part acts as a receiver for extracellular signals (conveyed via a modified sugar molecule, 3OC6HSL ) and produces an intracellular signal that other BioBrick parts can respond to. BioBrick parts communicate using RNA polymerase ; the more sugar fed to a receiver, the more polymerase it will emit each second 2. There is a direct analogy to electricity: Just as an ampere is the unit that describes how many electrons flow past any given point on a wire each second, polymerase per second, or PoPS, describes the rate at which polymerase

molecules flow down a DNA strand. The strength of the PoPS current controls how strongly a “plugged in” BioBrick part will respond. n A BioBrick nd. sequence recently developed by college students produces bubbles bbles of protein, called vesicles , inside a cell. Plugging the bubble BioBrick B Brick part into the PoPS current from a BioBrick receiver creates a new e genetic ew program 3 that can alter the number of vesicles created within n a cell; more sugar means more PoPS, which in turn produces more vesicles v and a more buoyant cell 4. This is but one example of a genetic program g gram made possible by standardized synthetic biological parts.

Cost of Commercial Gene Synthesis 20 18 16 14 12 10 8 6 4 2 0

$4-8 $10-16 $1-1.50

$2

$2-4

$1-2

2003

2004

2005

2006

4

Cumulative size of BioBrick i ioBrick dataBase

($ per base pair)

2002

...GATTACAG...

$0.75-1.25

2007

2008

As costs plummet, the largest barrier against more individuals taking advantage of DNA synthesis is the inherent complexity of biological systems. Just as software developers used to painstakingly program in binary machine language but now rely on software compilers and sophisticated programming languages, synthetic biologists today await powerful computer-aided abstraction tools that simplify biology’s complexity into easier formats. Many need to be developed.

2000 1800 1600 1400 1200 1000 800 600 400 200 0

# of Standard Parts 2000

400

200 12

2002

60

2003

1100

100

2004

2005

2006

2007

2008

Since BioBrick parts are open source and in the public ublic domain, anyone can use or modify existing BioBrick sequences free of charge and also submit new ones to online databases. atabases. This openness has driven significant growth in the number of BioBrick parts, as well as the creation of academic i contests like the annual international Genetically Engineered Machine ic (iGEM) competition. As more BioBrick sequences accumulate, the collective power of synthetic biology increases.

THE ISSUE: the democratization of Biotechnology If synthetic biologists continue crafting tools that simplify genetic engineering, it will become much easier for anyone, regardlesss of training, to construct novel biological systems. Synthetic biology techniques are “dual use”: The same methods that could lead to a cancer-fi fighting bacterium might also make deadly biological weapons; the same methods that promote ecologically unsound crop monocultures could uld also cause beneficial flowerings of engineered biological diversity. Ultimately, governments, large corporations, and international regulatory o bodies by ory themselves may not be able to control whether synthetic biology is wisely used—that choice will also be up to each of us.

Powerful new tools and technologies will ultimately give individuals the ability to design and modify custom genomes and construct artificial living organisms from scratch.

Seed’s Tear-outable tool for living in the 21st century

THE KEY QUESTIONS OF BIOFUELS:

CriBsheet #18

Are biofuels a viable replacement for fossil fuels? How are they made, and can their production be improved?

RISING ENERGY COSTS and concerns over climate change from emissions of CO2 have renewed interest in moving beyond fossil fuels. This is especially true where transportation is concerned, as it accounts for 70 percent of oil burned in the United States. Biofuels—fuels made from living things—are one potential replacement. Biofuels come in many forms, such as wood, manure, and animal and vegetable oils. Unlike fossil fuels, biofuels are renewable and potentially carbon-neutral: Burning a plant releases no more carbon than it absorbed while growing. In the US today’s predominant biofuel is ethanol. Typically produced from corn, American ethanol works as an alternative to gasoline in most cars and trucks. But cornbased ethanol may cause more problems than it solves.

pretreatment and extraction

GROWTH & HARVEST

GLUCOSE ENZYME (AMYLASE) STARCH

1

3

PRETREATMENT & EXTRACTION

CELLULOSE

2

4 6

Using the same crop as a source for both food and energy increases demand for it, which can cause rapid increases in food prices. When using corn, only the kernels are used and energy stored in other parts of the plant goes to waste. Fortunately, a more complex process can create ethanol from cellulose, the main component of plant stems and leaves; this process is less disruptive to the food supply and uses material that would otherwise be wasted. Though in theory ethanol can be carbon-neutral, in practice growing and harvesting corn or cellulose uses substantial amounts of fossil fuels. This

FERMENTATION YEAST

out of frying pan, into fire

5

ENZYMES

GLUCOSE

DISTILLATION

GLUCOSE

reliance on fossil fuels decreases the ratio of energy provided by the ethanol versus the energy spent in growing its source crop. While corn is easier than cellulose to convert into ethanol, it requires more resources to grow than many other cellulose sources. In general, using agricultural crops for biofuel poses problems of environmental degradation and resource depletion similar to those that occur in other forms of industrial agriculture.

After harvest, neither corn nor cellulose is immediately convertible to ethanol, which is a direct product of the sugar that’s extracted and fermented. Several different processes can extract sugar from corn and cellulose, but each requires pretreatment of the source material to make extraction easier. For corn, the kernels are milled to produce cornstarch 1, a mixture of two large molecules comprising chains of the sugar glucose; an enzyme called amylase then breaks down the mixture into glucose 2. Getting glucose from celluloserich plant material is more difficult. The material is pretreated with acids, steam, or ammonia to free the cellulose from plant-cell walls 3. Like starch, cellulose is made of chains of glucose molecules, but its molecules have far more bonds between them. And so, cellulose requires multiple enzymes to break up into glucose 4. Lignin, another component of plants, must be separated from the glucose-rich mixture before fermentation 5. Consequently, cellulosic ethanol production currently lags far behind ethanol production from corn, sugarcane, and other food crops.

fermentation and distillation

7

Biofuel Content of U.S. Gasoline Supply

making ethanol

Producing ethanol from either corn or cellulose requires four basic steps: growth and harvest, pretreatment and extraction of sugars, fermentation, and distillation.

Once the sugar is extracted from the cornstarch or cellulose, it is mixed with yeast or other microbes 6. The microbes ferment the sugar into alcohol, releasing carbon dioxide as a byproduct and leaving behind an unfermented mass called stillage, which can be recovered and used as a feed supplement for livestock. When fermentation is complete, the mixture is distilled and treated with chemicals to remove water, resulting in fuel-grade ethanol that can then be blended with gasoline and transported to pumping stations for distribution 7.

fossil fuels for Biofuels

150

BILLION GALLONS

Illustrator: Bryan Christie — www.bryanchristiedesign.com Writer: Lee Billings Graph data: Annual Energy Outlook 2008, US Department of Energy, Energy Information Administration. / A Farrell et al. (2006) “Ethanol Can Contribute to Energy and Environmental Goals.” Science 311:506-508

biofuels

MEGAJOULES OF FOSSIL ENERGY NEEDED TO PRODUCE EACH MEGAJOULE OF FUEL

100 0.10

50

0.774

Cellulosic Ethanol Ethanol Today

Biofuel content Fossil Fuel content 2006

2015

2030

As US biofuel production ramps up, more ethanol will be mixed with the gasoline supply. Even by 2030, however, fossil fuels are projected to remain the primary constituents of gasoline.

THE ISSUE: THE NEXT GENERATION OF BIOFUELS

1.19

Gasoline

Today both ethanol and gasoline production rely on energy from fossil fuels. Producing ethanol from cellulose rather than crops like corn will almost certainly require much less fossil-fuel energy.

The first generation of modern biofuels was made from food crops like corn because processing these plants is relatively easy, but their energy yields are low and their negative effects are many. “Second generation” biofuels like cellulosic ethanol are made from inedible materials like agricultural waste and wood chips, but their production has yet to be perfected, and the amount of energy they could deliver is unlikely to fulfill the entirety of our growing energy needs. Viable biofuels await us in the third generation or beyond, when highly energy-efficient production of fuel from algae or genetically modified microorganisms could become a reality.

Though promising as alternative energy sources, biofuels can have social, environmental, and energy costs rivaling those of fossil fuels. Future generations of biofuels may solve these problems.

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